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A tool for 3D genome and chromosome structural model construction

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Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts.

The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224).

This application is developed based on this thesis "Iterative reconstruction of three-dimensional model of human chromosomes from chromosomal contact data". (Ready for publication)

Gen3D Web Site


  • Use chromosomal contact data acquired using the Hi-C technique
  • Construct 3D structural genome and chromosome models from chromosomal contact data
  • Initialize the coordinates using probabilistic approach
  • Novel method to represent satisfied contacts in heat map matrix
  • Scoring schemes to figure out long range and short range contacts
  • Compared with other existing method and also validated with genome features


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